Variant report

Variant	rs6490409
Chromosome Location	chr13:30104154-30104155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30102776..30104828-chr13:30146774..30149345,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1018679	1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs1018682	0.98[EUR][1000 genomes]
rs12428026	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs1411928	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1571784	0.81[CEU][hapmap]
rs166828	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs1877463	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs2150688	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes]
rs2150690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[TSI][hapmap]
rs2150693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs2183717	0.95[CHB][hapmap]
rs2236499	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2277451	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2776957	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2776959	0.87[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2776963	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs2802248	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs2802249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs280922	0.81[CHB][hapmap]
rs280923	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs280930	0.81[CHB][hapmap]
rs280933	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs280934	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs280936	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs2989594	1.00[CHB][hapmap]
rs3011605	1.00[CHB][hapmap]
rs3783248	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs3783257	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3783259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3783260	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783261	1.00[ASN][1000 genomes]
rs3783262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783263	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3825536	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs476506	0.81[CHB][hapmap]
rs579451	0.81[CHB][hapmap]
rs617892	0.81[CHB][hapmap]
rs72623486	0.82[ASN][1000 genomes]
rs7997827	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs883055	0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs914362	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9550481	0.88[ASN][1000 genomes]
rs9550482	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs9551696	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs9578104	0.86[TSI][hapmap]
rs9579383	0.93[TSI][hapmap]
rs9579384	0.93[TSI][hapmap]
rs9579386	0.93[TSI][hapmap]
rs9579388	0.93[TSI][hapmap]
rs9579389	0.93[TSI][hapmap]
rs9579390	0.93[TSI][hapmap]
rs9579393	0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430551	chr13:30061100-30113000	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6490409	SHISA2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30071000-30128800	Strong transcription	Dnd41	blood
2	chr13:30082000-30106600	Weak transcription	Fetal Kidney	kidney
3	chr13:30082000-30107600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:30082800-30111600	Weak transcription	Stomach Mucosa	stomach
5	chr13:30083200-30107200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr13:30084200-30106000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr13:30084200-30107800	Strong transcription	Esophagus	oesophagus
8	chr13:30084200-30110400	Strong transcription	Fetal Intestine Small	intestine
9	chr13:30084200-30110600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr13:30084200-30112600	Strong transcription	NHEK	skin
11	chr13:30084200-30115800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr13:30084400-30111200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr13:30084600-30112200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:30084800-30110400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:30084800-30110600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr13:30084800-30111600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr13:30085000-30111600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr13:30085200-30104200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr13:30085600-30111200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr13:30085600-30111600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr13:30085800-30115400	Strong transcription	Primary T cells from cord blood	blood
22	chr13:30086000-30110600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr13:30086000-30111200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr13:30086600-30104800	Weak transcription	Fetal Brain Male	brain
25	chr13:30087000-30110200	Strong transcription	GM12878-XiMat	blood
26	chr13:30088000-30104600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr13:30089800-30110800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr13:30092200-30133000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr13:30092800-30106400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr13:30094000-30108000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr13:30095200-30112800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr13:30095400-30114800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr13:30095600-30110600	Strong transcription	Thymus	Thymus
34	chr13:30095800-30113200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr13:30096000-30110400	Strong transcription	NHLF	lung
36	chr13:30096000-30112600	Weak transcription	Psoas Muscle	Psoas
37	chr13:30096200-30107000	Strong transcription	Fetal Stomach	stomach
38	chr13:30096600-30106200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr13:30096600-30112200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr13:30096800-30111600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr13:30096800-30112200	Weak transcription	Liver	Liver
42	chr13:30097200-30138400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr13:30098000-30107000	Weak transcription	Adipose Nuclei	Adipose
44	chr13:30098000-30117200	Weak transcription	Small Intestine	intestine
45	chr13:30098400-30104800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr13:30098400-30110800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr13:30098800-30129000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr13:30099000-30114200	Weak transcription	Fetal Heart	heart
49	chr13:30099200-30105000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr13:30100000-30107200	Strong transcription	Fetal Thymus	thymus

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